Comparing normalized enrichment scores of cell-types between 2 groups of samples

[Manikgarg]

Hi,

I have two groups of samples and I want to check if a particular cell-type is enriched in one group compared to the other. Currently, I ran ConsensusTME on all the samples together using method 'ssgsea' and obtained normalized enrichment scores (NES) for all cell-types. For each cell-type, I then checked if there is any difference between NES of samples belonging to these two groups. Is this the correct way to approach it? Or shall I run ConsensusTME on these two groups separately and then compare their scores? Any suggestion appreciated :)

Thanks in advance!

Best, Manik

[Manikgarg]

Ohh actually just found the text explaining this in the manuscript

Finally, the output from ConsensusTME is NES scores, which accounts for variations in gene set size (14) and captures the relative level of estimated abundance of specific cell types across samples. For example, in a sample with a high NES score for a specific cell type, the individual genes of the gene set would rank higher in a sorted list of the abundance level of all genes in the transcriptome compared with samples with low NES score of the same cell type.

No worries, thanks again!